The overall goals of this project are to identify novel pathogens responsible for human disease and to create a flexible and highly effective system for the rapid identification and analysis of emerging or engineered agents. This will serve four purposes: (i) improve preparedness for outbreaks, (ii) characterize new viruses that we have already discovered in specimens from acutely ill patients (7 novel viruses identified to date), (iii) identify additional new pathogenic viruses, and (iv) provide new understanding of the human virome. To these ends, we have assembled an international collaborative team to systematically address the etiologies of a number of acute human illnesses using cutting edge molecular genomic approaches combined with classical immunological, virologic and epidemiologic methods. In this project, we will focus primarily on three diseases, encephalitis, respiratory tract infection, and gastroenteritis, which are collectively responsible for approximately 6,000,000 deaths annually. The most comprehensive analyses fail to identify and etiologic agent in 70% of encephalitis, -30% of respiratory tract infection and -40% of gastroenteritis. In addition, the emergence of new infectious agents, many of which manifest the clinical symptoms characteristic of these diseases, accentuates the critical need to define the complete spectrum of viruses capable of causing these diseases. In this proposal we present an integrated pipeline for identification of novel viruses, characterization of these viruses, and definition of their biological relevance. To identify novel viruses, two complementary genomic methodologies, pan-viral DNA microarrays and mass sequencing, will be applied to analyze clinical specimens in a highly comprehensive and minimally biased fashion. These methods have been previously used to identify SARS as a novel coronavirus during the 2003 outbreak, the novel WU polyomavirus and multiple novel viruses in stool from diarrhea patients. We will determine the genomic structure and biological relevance of novel viruses using molecular, epidemiological, and seroepidemiological criteria. Viruses that appear to be relevant will then be prioritized for future studies aimed at elucidating both the basic biology of the viruses as well as their potential pathogenicity.